@nucacidhunter, was this an identical pool in terms of bacterial biomass and complexity? We've seen variation in sequencing quality for some amplicon libraries that probably had more off-target amplification due to low amount of true template.

It seems more cost effective to use the 600 cycle v3 kit in place of a 500 cycle v2 kit (and simply run a 2x250)...any thoughts?

I have shown the general trend and these are amplicons prepared using two step PCR so the initial cycles for both read 1 and 2 includes primer sequences. Pool of 96 libraries are sequenced in one flow cell and because they are targeting the same region diversity always is low. I like V3 because the yields are higher than V2 reagents.

Illumina announced a Q30 performance back to the "normal" for the "long read" kits (600 cycles V3 and 500 cycles V2) since november 2017.
But since this announcement, I runned 4 runs 600 cycles V3 with still Q30 bad quality. Their tech support agreeded that it is still because of a sequencing kit reagents issue.

in our experience the reagent quality has gotten better, but is still not as good as 3 years ago and we still see our low quality run outliers (that should have performed better according to cluster density). We are running almost exclusively amplicons.

I sent them all the lot numbers, but they didn't give me the informations about "new or old chemistry". But the kit were sent on december, so I guess new one? This is why I was asking to have others feedbacks...
We are also running amplicons and small genomes too. And those 4 runs also had a good cluster density, so it is not because of over clustered runs.
Thanks for your replies, I hope that the Q30 quality will be better in few weeks!